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Gut Microbes. 2014 Mar-Apr;5(2):192-201. doi: 10.4161/gmic.28442. Epub 2014 Mar 5.

Early life establishment of site-specific microbial communities in the gut.

Author information

1
Department of Pediatrics; Vanderbilt University; Nashville, TN USA.
2
Department of Pediatrics; Vanderbilt University; Nashville, TN USA; Department of Pathology, Microbiology, and Immunology; Vanderbilt University; Nashville, TN USA.
3
Genome Technology Center; Stanford University; Palo Alto, CA USA.
4
Department of Biological Sciences; Vanderbilt University; Nashville, TN USA.
5
Department of Biostatistics; Vanderbilt University; Nashville, TN USA.
6
Department of Pathology, Microbiology, and Immunology; Vanderbilt University; Nashville, TN USA.
7
Department of Pediatric Surgery; Vanderbilt University; Nashville, TN USA.
8
Department of Pathology, Microbiology, and Immunology; Vanderbilt University; Nashville, TN USA; Department of Laboratory Medicine; Memorial Sloan-Kettering Cancer Center; New York, NY USA.
9
Department of Pathology, Microbiology, and Immunology; Vanderbilt University; Nashville, TN USA; Department of Biological Sciences; Vanderbilt University; Nashville, TN USA.
10
Department of Medicine; Division of Genomic Medicine; Vanderbilt University; Nashville, TN USA.

Abstract

Fecal sampling is widely utilized to define small intestinal tissue-level microbial communities in healthy and diseased newborns. However, this approach may lead to inaccurate assessments of disease or therapeutics in newborns because of the assumption that the taxa in the fecal microbiota are representative of the taxa present throughout the gastrointestinal tract. To assess the stratification of microbes in the newborn gut and to evaluate the probable shortcoming of fecal sampling in place of tissue sampling, we simultaneously compared intestinal mucosa and fecal microbial communities in 15 neonates undergoing intestinal resections. We report three key results. First, when the site of fecal and mucosal samples are further apart, their microbial communities are more distinct, as indicated by low mean Sørensen similarity indices for each patient's fecal and tissue microbiota. Second, two distinct niches (intestinal mucosa and fecal microbiota) are evident by principal component analyses, demonstrating the critical role of sample source in defining microbial composition. Finally, in contrast to adult studies, intestinal bacterial diversity was higher in tissue than in fecal samples. This study represents an unprecedented map of the infant microbiota from intestinal mucosa and establishes discernable biogeography throughout the neonatal gastrointestinal tract. Our results question the reliance on fecal microbiota as a proxy for the developing intestinal microbiota. Additionally, the robust intestinal tissue-level bacterial diversity we detected at these early ages may contribute to the maturation of mucosal immunity.

KEYWORDS:

fecal microbiome; host-microbial interactions; intestinal bacterial diversity; mucosal immunity; neonatal microbiome

PMID:
24637795
PMCID:
PMC4063844
DOI:
10.4161/gmic.28442
[Indexed for MEDLINE]
Free PMC Article

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